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Using Synthetic Biology to Engineer Living Cells That Interface with Programmable Materials
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A programmable biomolecular computing machine with bacterial phenotype output.

Elizaveta Kossoy1, Noa Lavid, Michal Soreni-Harari

  • 1Schulich Faculty of Chemistry and Institute of Catalysis Science and Technology, Technion--Israel Institute of Technology, Technion City, Haifa 32000, Israel.

Chembiochem : a European Journal of Chemical Biology
|June 15, 2007
PubMed
Summary

Molecular computers compute using DNA, directly interfacing with biology. This study shows DNA computation output can be a visible bacterial color change, distinguishing between "accepting" and "unaccepting" states.

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Area of Science:

  • Biomolecular computing
  • Synthetic biology
  • DNA nanotechnology

Background:

  • Molecular computers offer direct biological system interaction without interfaces.
  • All components (hardware, software, input, output) are molecules in solution.
  • Programmable chemical events drive molecular computations.

Purpose of the Study:

  • To demonstrate a visible bacterial phenotype as the output of molecular finite automaton computation.
  • To link DNA-based computation states to observable bacterial characteristics.

Main Methods:

  • Designed a 2-symbol-2-state finite automaton using linear double-stranded DNA inputs.
  • Inserted DNA symbols into the lacZ gene on a pUC18 plasmid.
  • Transformed E. coli with resultant plasmids and observed colony color on X-gal medium.

Main Results:

  • Computation produced circular plasmids with either a 9 base pair (accepting) or 11 base pair (unaccepting) insert in lacZ.
  • Accepting state resulted in functional beta-galactosidase and blue colonies.
  • Unaccepting state caused white colonies due to an open reading frame shift.

Conclusions:

  • Demonstrated visible bacterial phenotypes as a direct output of molecular computation.
  • Established a link between DNA sequence manipulation and observable cellular function.
  • Showcased the potential of biomolecular devices for biological sensing and computation.